org.strbio.local
Class PDB

java.lang.Object
  extended by org.strbio.local.PDB

public class PDB
extends java.lang.Object

Class to access a local copy of the PDB. Classes to read PDB or DSSP files as Proteins are found in ProteinSet.

  Version 1.2, 11/14/02 - added support for SCOP-style names
  Version 1.1, 7/28/99 - adapted to new PDBInfo structure
  Version 1.0, 7/22/99 - original version
  

Version:
1.2, 11/14/02
Author:
JMC
See Also:
ProteinSet

Field Summary
static java.lang.String DEFAULT_PDB_PATH
          The default PDB path for all users of this library.
 
Constructor Summary
PDB()
           
 
Method Summary
static java.lang.String findPDBName(java.lang.String name, Printf outfile)
          Find PDB file corresponding to a given protein name.
static PDBInfo getInfo(java.lang.String name, Printf outfile)
          Gets info on a PDB file for a given PDB code.
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

DEFAULT_PDB_PATH

public static final java.lang.String DEFAULT_PDB_PATH
The default PDB path for all users of this library. This is system-dependent.

See Also:
Constant Field Values
Constructor Detail

PDB

public PDB()
Method Detail

findPDBName

public static final java.lang.String findPDBName(java.lang.String name,
                                                 Printf outfile)
Find PDB file corresponding to a given protein name. Looks for a property called pdb.path in ~/.pdb.properties. If this is not found, it uses the default pdb path. This is a colon or semicolon separated string listing directories you want to look for PDB files. Each of these directories can have subdirectories with proteins sorted by the first letter or first 2 letters of the PDB code. The order of searching each directory is as follows:
  1. exact name (i.e. 1abc)
  2. name with .pdb appended to it (1abc -> 1abc.pdb)
  3. 1abc or 1ABC -> pdb1abc.ent
  4. 1abc or 1ABC -> ab/pdb1abc.ent
  5. 1abc or 1ABC -> a/pdb1abc.ent
  6. All of above, with first character truncated, i.e. d2minb_ treated like 2min
Also, all combinations ending in .gz are checked.


getInfo

public static final PDBInfo getInfo(java.lang.String name,
                                    Printf outfile)
Gets info on a PDB file for a given PDB code.